Chemoproteomic target-class drug discovery against the deubiquitinating enzymes

Abstract

Modern small molecule drug discovery is dominated, and subsequently limited by a paradigm of reversible non-covalent inhibitors. The deubiquitinating enzymes (DUBs) is a class of ~100 proteases that regulate normal and pathophysiological processes through cleaving ubiquitin marks from protein substrates and is underserved by this existing paradigm. Despite intense interest, a lack of selective inhibitors and design principles impede biological investigation. Here, we develop a DUB target-class inhibitor discovery platform consisting of a tailored covalent small molecule library, mass spectrometry chemoproteomics, and a suite of orthogonal validation assays. We first demonstrate small-scale proof-of-concept and subsequent improvements (chapter 2), then apply the platform for a screening campaign to identify and validate novel DUB covalent ligands (chapter 3). This has led to a revision of statistical approaches for handling chemoproteomic screening data (chapter 4). Our systematic interrogation provides a methodological roadmap for future target-class campaigns, guiding principles for DUB-targeting medicinal chemistry, attractive chemical starting points for diverse DUBs and a first-in-class probe for studying the understudied DUB VCPIP1.